HEADER LYASE 18-NOV-15 5EUD
TITLE S1P LYASE BACTERIAL SURROGATE BOUND TO N-(1-(4-(3-HYDROXYPROP-1-YN-1-
TITLE 2 YL)PHENYL)-2-((4-METHOXY-2,5-DIMETHYLBENZYL)AMINO)ETHYL)-5-
TITLE 3 METHYLISOXAZOLE-3-CARBOXAMIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PUTATIVE SPHINGOSINE-1-PHOSPHATE LYASE;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SYMBIOBACTERIUM THERMOPHILUM (STRAIN T / IAM
SOURCE 3 14863);
SOURCE 4 ORGANISM_TAXID: 292459;
SOURCE 5 STRAIN: T / IAM 14863;
SOURCE 6 GENE: STH1274;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS S1P LYASE BACTERIAL SURROGATE, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.A.ARGIRIADI,D.BANACH,E.RADZIEJEWSKA,S.MARCHIE,J.DIMAURO,J.DINGES,
AUTHOR 2 E.DOMINGUEZ,C.HUTCHINS,R.A.JUDGE,K.QUEENEY,G.WALLACE,C.M.HARRIS
REVDAT 6 15-NOV-23 5EUD 1 REMARK
REVDAT 5 27-SEP-23 5EUD 1 REMARK
REVDAT 4 20-JUL-16 5EUD 1 REMARK
REVDAT 3 27-APR-16 5EUD 1 JRNL
REVDAT 2 06-APR-16 5EUD 1 JRNL
REVDAT 1 16-MAR-16 5EUD 0
JRNL AUTH M.A.ARGIRIADI,D.BANACH,E.RADZIEJEWSKA,S.MARCHIE,J.DIMAURO,
JRNL AUTH 2 J.DINGES,E.DOMINGUEZ,C.HUTCHINS,R.A.JUDGE,K.QUEENEY,
JRNL AUTH 3 G.WALLACE,C.M.HARRIS
JRNL TITL CREATION OF A S1P LYASE BACTERIAL SURROGATE FOR
JRNL TITL 2 STRUCTURE-BASED DRUG DESIGN.
JRNL REF BIOORG.MED.CHEM.LETT. V. 26 2293 2016
JRNL REFN ESSN 1464-3405
JRNL PMID 27013389
JRNL DOI 10.1016/J.BMCL.2016.02.084
REMARK 2
REMARK 2 RESOLUTION. 2.24 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.5
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.75
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 45295
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.164
REMARK 3 R VALUE (WORKING SET) : 0.162
REMARK 3 FREE R VALUE : 0.206
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040
REMARK 3 FREE R VALUE TEST SET COUNT : 2282
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.30
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3300
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2072
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3131
REMARK 3 BIN R VALUE (WORKING SET) : 0.2045
REMARK 3 BIN FREE R VALUE : 0.2567
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.12
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 169
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6854
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 76
REMARK 3 SOLVENT ATOMS : 423
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 37.48
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.79
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.93350
REMARK 3 B22 (A**2) : 0.95940
REMARK 3 B33 (A**2) : -2.89290
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.212
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.260
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.186
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.247
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.186
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 7127 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 9740 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 2245 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 123 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 1094 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 7127 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 904 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 8597 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.09
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.32
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.79
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5EUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-15.
REMARK 100 THE DEPOSITION ID IS D_1000215237.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 14-MAR-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 17-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : AUTOPROC
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45469
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240
REMARK 200 RESOLUTION RANGE LOW (A) : 64.800
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 6.600
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.14000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 3EUE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.73
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% (W/V) PEG 3350, 0.05M BIS-TRIS,
REMARK 280 PH 6.5, VAPOR DIFFUSION, TEMPERATURE 296K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 41.97000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.75350
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.56300
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.75350
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.97000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.56300
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 14110 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 29290 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 0
REMARK 465 PRO A 1
REMARK 465 LEU A 2
REMARK 465 SER A 3
REMARK 465 ALA A 4
REMARK 465 PHE A 5
REMARK 465 SER A 6
REMARK 465 PRO A 7
REMARK 465 PRO A 8
REMARK 465 LEU A 9
REMARK 465 PRO A 10
REMARK 465 CYS A 11
REMARK 465 ASP A 12
REMARK 465 PRO A 13
REMARK 465 ALA A 14
REMARK 465 ARG A 15
REMARK 465 SER A 16
REMARK 465 HIS A 17
REMARK 465 PRO A 18
REMARK 465 THR A 19
REMARK 465 PRO A 20
REMARK 465 GLU A 21
REMARK 465 PHE A 22
REMARK 465 PRO A 23
REMARK 465 SER A 24
REMARK 465 SER A 25
REMARK 465 LEU A 26
REMARK 465 GLN A 27
REMARK 465 ASP A 28
REMARK 465 TYR A 29
REMARK 465 CYS A 30
REMARK 465 GLU A 31
REMARK 465 ILE A 32
REMARK 465 ARG A 33
REMARK 465 GLY A 34
REMARK 465 ILE A 35
REMARK 465 GLN A 36
REMARK 465 SER A 37
REMARK 465 GLN A 38
REMARK 465 PRO A 39
REMARK 465 PRO A 40
REMARK 465 ALA A 41
REMARK 465 ARG A 42
REMARK 465 ARG A 43
REMARK 465 ASP A 44
REMARK 465 PRO A 45
REMARK 465 THR A 46
REMARK 465 MET A 47
REMARK 465 ASP A 48
REMARK 465 TRP A 49
REMARK 465 LEU A 50
REMARK 465 ALA A 51
REMARK 465 SER A 52
REMARK 465 LEU A 53
REMARK 465 ARG A 54
REMARK 465 HIS A 509
REMARK 465 HIS A 510
REMARK 465 HIS A 511
REMARK 465 HIS A 512
REMARK 465 HIS A 513
REMARK 465 MET B 0
REMARK 465 PRO B 1
REMARK 465 LEU B 2
REMARK 465 SER B 3
REMARK 465 ALA B 4
REMARK 465 PHE B 5
REMARK 465 SER B 6
REMARK 465 PRO B 7
REMARK 465 PRO B 8
REMARK 465 LEU B 9
REMARK 465 PRO B 10
REMARK 465 CYS B 11
REMARK 465 ASP B 12
REMARK 465 PRO B 13
REMARK 465 ALA B 14
REMARK 465 ARG B 15
REMARK 465 SER B 16
REMARK 465 HIS B 17
REMARK 465 PRO B 18
REMARK 465 THR B 19
REMARK 465 PRO B 20
REMARK 465 GLU B 21
REMARK 465 PHE B 22
REMARK 465 PRO B 23
REMARK 465 SER B 24
REMARK 465 SER B 25
REMARK 465 LEU B 26
REMARK 465 GLN B 27
REMARK 465 ASP B 28
REMARK 465 TYR B 29
REMARK 465 CYS B 30
REMARK 465 GLU B 31
REMARK 465 ILE B 32
REMARK 465 ARG B 33
REMARK 465 GLY B 34
REMARK 465 ILE B 35
REMARK 465 GLN B 36
REMARK 465 SER B 37
REMARK 465 GLN B 38
REMARK 465 PRO B 39
REMARK 465 PRO B 40
REMARK 465 ALA B 41
REMARK 465 ARG B 42
REMARK 465 ARG B 43
REMARK 465 ASP B 44
REMARK 465 PRO B 45
REMARK 465 THR B 46
REMARK 465 MET B 47
REMARK 465 ASP B 48
REMARK 465 TRP B 49
REMARK 465 LEU B 50
REMARK 465 ALA B 51
REMARK 465 SER B 52
REMARK 465 LEU B 53
REMARK 465 ARG B 54
REMARK 465 SER B 55
REMARK 465 GLN B 56
REMARK 465 ILE B 57
REMARK 465 LYS B 58
REMARK 465 HIS B 508
REMARK 465 HIS B 509
REMARK 465 HIS B 510
REMARK 465 HIS B 511
REMARK 465 HIS B 512
REMARK 465 HIS B 513
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ALA A 103 -56.60 64.18
REMARK 500 HIS A 106 -76.45 -100.86
REMARK 500 HIS A 129 70.96 -111.72
REMARK 500 TRP A 133 66.59 -119.12
REMARK 500 ILE A 281 -52.96 -120.03
REMARK 500 ASP A 296 -150.71 -125.51
REMARK 500 LLP A 311 -112.20 -98.26
REMARK 500 TRP A 406 -12.21 -152.04
REMARK 500 ARG B 61 -55.38 -28.79
REMARK 500 ALA B 103 -56.04 62.71
REMARK 500 HIS B 106 -74.02 -106.56
REMARK 500 HIS B 129 78.33 -112.00
REMARK 500 ASP B 296 -152.14 -117.94
REMARK 500 LLP B 311 -113.38 -104.95
REMARK 500 THR B 349 -161.61 -128.44
REMARK 500 TRP B 406 -9.16 -154.29
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5S6 A 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5S6 A 603
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 601
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5EUE RELATED DB: PDB
DBREF 5EUD A 2 507 UNP Q67PY4 Q67PY4_SYMTH 2 507
DBREF 5EUD B 2 507 UNP Q67PY4 Q67PY4_SYMTH 2 507
SEQADV 5EUD MET A 0 UNP Q67PY4 INITIATING METHIONINE
SEQADV 5EUD PRO A 1 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD PHE A 249 UNP Q67PY4 TYR 249 ENGINEERED MUTATION
SEQADV 5EUD ILE A 344 UNP Q67PY4 LEU 344 ENGINEERED MUTATION
SEQADV 5EUD ALA A 346 UNP Q67PY4 PHE 346 ENGINEERED MUTATION
SEQADV 5EUD SER A 497 UNP Q67PY4 LEU 497 ENGINEERED MUTATION
SEQADV 5EUD HIS A 508 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS A 509 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS A 510 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS A 511 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS A 512 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS A 513 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD MET B 0 UNP Q67PY4 INITIATING METHIONINE
SEQADV 5EUD PRO B 1 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD PHE B 249 UNP Q67PY4 TYR 249 ENGINEERED MUTATION
SEQADV 5EUD ILE B 344 UNP Q67PY4 LEU 344 ENGINEERED MUTATION
SEQADV 5EUD ALA B 346 UNP Q67PY4 PHE 346 ENGINEERED MUTATION
SEQADV 5EUD SER B 497 UNP Q67PY4 LEU 497 ENGINEERED MUTATION
SEQADV 5EUD HIS B 508 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS B 509 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS B 510 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS B 511 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS B 512 UNP Q67PY4 EXPRESSION TAG
SEQADV 5EUD HIS B 513 UNP Q67PY4 EXPRESSION TAG
SEQRES 1 A 514 MET PRO LEU SER ALA PHE SER PRO PRO LEU PRO CYS ASP
SEQRES 2 A 514 PRO ALA ARG SER HIS PRO THR PRO GLU PHE PRO SER SER
SEQRES 3 A 514 LEU GLN ASP TYR CYS GLU ILE ARG GLY ILE GLN SER GLN
SEQRES 4 A 514 PRO PRO ALA ARG ARG ASP PRO THR MET ASP TRP LEU ALA
SEQRES 5 A 514 SER LEU ARG SER GLN ILE LYS PRO TYR ARG ASP ARG PHE
SEQRES 6 A 514 PRO SER HIS ALA ARG LEU PRO ARG ALA GLY LEU PRO ARG
SEQRES 7 A 514 ALA GLU ILE LEU ALA GLU ILE ALA ALA MET GLY ALA ALA
SEQRES 8 A 514 GLU SER PRO ALA TRP ARG ASP GLY TYR ALA SER GLY ALA
SEQRES 9 A 514 VAL TYR HIS GLY ASP GLU HIS HIS ILE ALA PHE LEU ASN
SEQRES 10 A 514 GLU VAL TYR ALA LEU GLN SER GLN SER ASN PRO LEU HIS
SEQRES 11 A 514 PRO ASP LEU TRP PRO SER THR ALA LYS PHE GLU ALA GLU
SEQRES 12 A 514 VAL VAL ALA MET THR ALA HIS MET LEU GLY GLY ASP ALA
SEQRES 13 A 514 ALA GLY GLY THR VAL CYS GLY THR VAL THR SER GLY GLY
SEQRES 14 A 514 THR GLU SER LEU LEU LEU ALA MET LYS THR TYR ARG ASP
SEQRES 15 A 514 TRP ALA ARG ALA THR LYS GLY ILE THR ALA PRO GLU ALA
SEQRES 16 A 514 VAL VAL PRO VAL SER ALA HIS ALA ALA PHE ASP LYS ALA
SEQRES 17 A 514 ALA GLN TYR PHE GLY ILE LYS LEU VAL ARG THR PRO LEU
SEQRES 18 A 514 ASP ALA ASP TYR ARG ALA ASP VAL ALA ALA MET ARG GLU
SEQRES 19 A 514 ALA ILE THR PRO ASN THR VAL VAL VAL ALA GLY SER ALA
SEQRES 20 A 514 PRO GLY PHE PRO HIS GLY VAL VAL ASP PRO ILE PRO GLU
SEQRES 21 A 514 ILE ALA ALA LEU ALA ALA GLU HIS GLY ILE GLY CYS HIS
SEQRES 22 A 514 VAL ASP ALA CYS LEU GLY GLY PHE ILE LEU PRO TRP ALA
SEQRES 23 A 514 GLU ARG LEU GLY TYR PRO VAL PRO PRO PHE ASP PHE ARG
SEQRES 24 A 514 LEU GLU GLY VAL THR SER VAL SER ALA ASP THR HIS LLP
SEQRES 25 A 514 TYR GLY TYR GLY ALA LYS GLY THR SER VAL ILE LEU TYR
SEQRES 26 A 514 ARG ARG PRO ASP LEU LEU HIS TYR GLN TYR PHE ILE ALA
SEQRES 27 A 514 ALA ASP TRP PRO GLY GLY ILE TYR ALA SER PRO THR PHE
SEQRES 28 A 514 ALA GLY SER ARG PRO GLY ALA LEU SER ALA THR ALA TRP
SEQRES 29 A 514 ALA ALA MET LEU SER LEU GLY GLU GLU GLY TYR LEU ASP
SEQRES 30 A 514 ALA THR ARG ARG ILE LEU GLN ALA ALA ASP ARG LEU LYS
SEQRES 31 A 514 ALA GLY VAL ARG ALA ILE PRO SER LEU LYS ILE LEU GLY
SEQRES 32 A 514 ASP PRO LEU TRP VAL ILE ALA VAL ALA SER ASP GLU LEU
SEQRES 33 A 514 ASN ILE TYR GLN VAL MET GLU GLU MET ALA GLY ARG GLY
SEQRES 34 A 514 TRP ARG LEU ASN GLY LEU HIS ARG PRO PRO ALA PHE HIS
SEQRES 35 A 514 VAL ALA LEU THR LEU ARG HIS THR GLU PRO GLY VAL VAL
SEQRES 36 A 514 ASP ARG PHE LEU ALA ASP LEU GLN ASP ALA VAL ALA GLN
SEQRES 37 A 514 VAL ARG ALA HIS PRO GLU LYS ALA THR GLY MET ALA PRO
SEQRES 38 A 514 VAL TYR GLY MET ALA ALA ALA ALA PRO PRO GLU LEU VAL
SEQRES 39 A 514 ARG GLN VAL SER THR GLY PHE ILE ASP LEU LEU TYR GLU
SEQRES 40 A 514 VAL HIS HIS HIS HIS HIS HIS
SEQRES 1 B 514 MET PRO LEU SER ALA PHE SER PRO PRO LEU PRO CYS ASP
SEQRES 2 B 514 PRO ALA ARG SER HIS PRO THR PRO GLU PHE PRO SER SER
SEQRES 3 B 514 LEU GLN ASP TYR CYS GLU ILE ARG GLY ILE GLN SER GLN
SEQRES 4 B 514 PRO PRO ALA ARG ARG ASP PRO THR MET ASP TRP LEU ALA
SEQRES 5 B 514 SER LEU ARG SER GLN ILE LYS PRO TYR ARG ASP ARG PHE
SEQRES 6 B 514 PRO SER HIS ALA ARG LEU PRO ARG ALA GLY LEU PRO ARG
SEQRES 7 B 514 ALA GLU ILE LEU ALA GLU ILE ALA ALA MET GLY ALA ALA
SEQRES 8 B 514 GLU SER PRO ALA TRP ARG ASP GLY TYR ALA SER GLY ALA
SEQRES 9 B 514 VAL TYR HIS GLY ASP GLU HIS HIS ILE ALA PHE LEU ASN
SEQRES 10 B 514 GLU VAL TYR ALA LEU GLN SER GLN SER ASN PRO LEU HIS
SEQRES 11 B 514 PRO ASP LEU TRP PRO SER THR ALA LYS PHE GLU ALA GLU
SEQRES 12 B 514 VAL VAL ALA MET THR ALA HIS MET LEU GLY GLY ASP ALA
SEQRES 13 B 514 ALA GLY GLY THR VAL CYS GLY THR VAL THR SER GLY GLY
SEQRES 14 B 514 THR GLU SER LEU LEU LEU ALA MET LYS THR TYR ARG ASP
SEQRES 15 B 514 TRP ALA ARG ALA THR LYS GLY ILE THR ALA PRO GLU ALA
SEQRES 16 B 514 VAL VAL PRO VAL SER ALA HIS ALA ALA PHE ASP LYS ALA
SEQRES 17 B 514 ALA GLN TYR PHE GLY ILE LYS LEU VAL ARG THR PRO LEU
SEQRES 18 B 514 ASP ALA ASP TYR ARG ALA ASP VAL ALA ALA MET ARG GLU
SEQRES 19 B 514 ALA ILE THR PRO ASN THR VAL VAL VAL ALA GLY SER ALA
SEQRES 20 B 514 PRO GLY PHE PRO HIS GLY VAL VAL ASP PRO ILE PRO GLU
SEQRES 21 B 514 ILE ALA ALA LEU ALA ALA GLU HIS GLY ILE GLY CYS HIS
SEQRES 22 B 514 VAL ASP ALA CYS LEU GLY GLY PHE ILE LEU PRO TRP ALA
SEQRES 23 B 514 GLU ARG LEU GLY TYR PRO VAL PRO PRO PHE ASP PHE ARG
SEQRES 24 B 514 LEU GLU GLY VAL THR SER VAL SER ALA ASP THR HIS LLP
SEQRES 25 B 514 TYR GLY TYR GLY ALA LYS GLY THR SER VAL ILE LEU TYR
SEQRES 26 B 514 ARG ARG PRO ASP LEU LEU HIS TYR GLN TYR PHE ILE ALA
SEQRES 27 B 514 ALA ASP TRP PRO GLY GLY ILE TYR ALA SER PRO THR PHE
SEQRES 28 B 514 ALA GLY SER ARG PRO GLY ALA LEU SER ALA THR ALA TRP
SEQRES 29 B 514 ALA ALA MET LEU SER LEU GLY GLU GLU GLY TYR LEU ASP
SEQRES 30 B 514 ALA THR ARG ARG ILE LEU GLN ALA ALA ASP ARG LEU LYS
SEQRES 31 B 514 ALA GLY VAL ARG ALA ILE PRO SER LEU LYS ILE LEU GLY
SEQRES 32 B 514 ASP PRO LEU TRP VAL ILE ALA VAL ALA SER ASP GLU LEU
SEQRES 33 B 514 ASN ILE TYR GLN VAL MET GLU GLU MET ALA GLY ARG GLY
SEQRES 34 B 514 TRP ARG LEU ASN GLY LEU HIS ARG PRO PRO ALA PHE HIS
SEQRES 35 B 514 VAL ALA LEU THR LEU ARG HIS THR GLU PRO GLY VAL VAL
SEQRES 36 B 514 ASP ARG PHE LEU ALA ASP LEU GLN ASP ALA VAL ALA GLN
SEQRES 37 B 514 VAL ARG ALA HIS PRO GLU LYS ALA THR GLY MET ALA PRO
SEQRES 38 B 514 VAL TYR GLY MET ALA ALA ALA ALA PRO PRO GLU LEU VAL
SEQRES 39 B 514 ARG GLN VAL SER THR GLY PHE ILE ASP LEU LEU TYR GLU
SEQRES 40 B 514 VAL HIS HIS HIS HIS HIS HIS
MODRES 5EUD LLP A 311 LYS MODIFIED RESIDUE
MODRES 5EUD LLP B 311 LYS MODIFIED RESIDUE
HET LLP A 311 24
HET LLP B 311 24
HET PO4 A 601 5
HET 5S6 A 602 33
HET 5S6 A 603 33
HET PO4 B 601 5
HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-
HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4-
HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID
HETNAM PO4 PHOSPHATE ION
HETNAM 5S6 ~{N}-[(1~{S})-2-[(4-METHOXY-2,5-DIMETHYL-PHENYL)
HETNAM 2 5S6 METHYLAMINO]-1-[4-(3-OXIDANYLPROP-1-YNYL)
HETNAM 3 5S6 PHENYL]ETHYL]-5-METHYL-1,2-OXAZOLE-3-CARBOXAMIDE
HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE
FORMUL 1 LLP 2(C14 H22 N3 O7 P)
FORMUL 3 PO4 2(O4 P 3-)
FORMUL 4 5S6 2(C26 H29 N3 O4)
FORMUL 7 HOH *423(H2 O)
HELIX 1 AA1 PRO A 76 ASP A 97 1 22
HELIX 2 AA2 ASP A 108 SER A 123 1 16
HELIX 3 AA3 TRP A 133 LEU A 151 1 19
HELIX 4 AA4 GLY A 152 GLY A 157 5 6
HELIX 5 AA5 GLY A 167 GLY A 188 1 22
HELIX 6 AA6 ALA A 202 GLY A 212 1 11
HELIX 7 AA7 ASP A 227 ILE A 235 1 9
HELIX 8 AA8 PRO A 256 GLY A 268 1 13
HELIX 9 AA9 ILE A 281 LEU A 288 1 8
HELIX 10 AB1 ARG A 326 HIS A 331 1 6
HELIX 11 AB2 TYR A 332 TYR A 334 5 3
HELIX 12 AB3 PRO A 355 ARG A 393 1 39
HELIX 13 AB4 ASN A 416 ARG A 427 1 12
HELIX 14 AB5 THR A 445 GLU A 450 5 6
HELIX 15 AB6 GLY A 452 HIS A 471 1 20
HELIX 16 AB7 MET A 478 ALA A 488 1 11
HELIX 17 AB8 PRO A 489 GLU A 506 1 18
HELIX 18 AB9 PRO B 76 ASP B 97 1 22
HELIX 19 AC1 ASP B 108 SER B 123 1 16
HELIX 20 AC2 TRP B 133 LEU B 151 1 19
HELIX 21 AC3 GLY B 152 GLY B 157 5 6
HELIX 22 AC4 GLY B 167 GLY B 188 1 22
HELIX 23 AC5 ALA B 202 GLY B 212 1 11
HELIX 24 AC6 ASP B 227 ILE B 235 1 9
HELIX 25 AC7 PRO B 256 GLY B 268 1 13
HELIX 26 AC8 ILE B 281 LEU B 288 1 8
HELIX 27 AC9 ARG B 326 HIS B 331 1 6
HELIX 28 AD1 PRO B 355 ALA B 394 1 40
HELIX 29 AD2 ASN B 416 ARG B 427 1 12
HELIX 30 AD3 THR B 445 GLU B 450 5 6
HELIX 31 AD4 GLY B 452 HIS B 471 1 20
HELIX 32 AD5 MET B 478 ALA B 488 1 11
HELIX 33 AD6 PRO B 489 TYR B 505 1 17
SHEET 1 AA1 7 CYS A 161 THR A 165 0
SHEET 2 AA1 7 SER A 320 TYR A 324 -1 O TYR A 324 N CYS A 161
SHEET 3 AA1 7 SER A 304 ALA A 307 -1 N VAL A 305 O LEU A 323
SHEET 4 AA1 7 GLY A 270 ASP A 274 1 N VAL A 273 O SER A 304
SHEET 5 AA1 7 THR A 239 SER A 245 1 N GLY A 244 O ASP A 274
SHEET 6 AA1 7 GLU A 193 PRO A 197 1 N GLU A 193 O VAL A 240
SHEET 7 AA1 7 LYS A 214 THR A 218 1 O VAL A 216 N ALA A 194
SHEET 1 AA2 2 PHE A 335 ALA A 337 0
SHEET 2 AA2 2 TYR A 345 SER A 347 -1 O TYR A 345 N ALA A 337
SHEET 1 AA3 4 LYS A 399 ILE A 400 0
SHEET 2 AA3 4 VAL A 407 ALA A 411 -1 O ALA A 411 N LYS A 399
SHEET 3 AA3 4 ALA A 439 ALA A 443 -1 O VAL A 442 N ILE A 408
SHEET 4 AA3 4 ASN A 432 LEU A 434 -1 N LEU A 434 O ALA A 439
SHEET 1 AA4 7 CYS B 161 THR B 165 0
SHEET 2 AA4 7 SER B 320 TYR B 324 -1 O TYR B 324 N CYS B 161
SHEET 3 AA4 7 SER B 304 ALA B 307 -1 N VAL B 305 O LEU B 323
SHEET 4 AA4 7 GLY B 270 ASP B 274 1 N VAL B 273 O SER B 304
SHEET 5 AA4 7 THR B 239 SER B 245 1 N GLY B 244 O ASP B 274
SHEET 6 AA4 7 GLU B 193 PRO B 197 1 N GLU B 193 O VAL B 240
SHEET 7 AA4 7 LYS B 214 THR B 218 1 O VAL B 216 N ALA B 194
SHEET 1 AA5 2 PHE B 335 ALA B 337 0
SHEET 2 AA5 2 TYR B 345 SER B 347 -1 O TYR B 345 N ALA B 337
SHEET 1 AA6 4 LYS B 399 ILE B 400 0
SHEET 2 AA6 4 VAL B 407 ALA B 411 -1 O ALA B 411 N LYS B 399
SHEET 3 AA6 4 ALA B 439 ALA B 443 -1 O PHE B 440 N VAL B 410
SHEET 4 AA6 4 ASN B 432 LEU B 434 -1 N LEU B 434 O ALA B 439
LINK C HIS A 310 N LLP A 311 1555 1555 1.34
LINK C LLP A 311 N TYR A 312 1555 1555 1.35
LINK C HIS B 310 N LLP B 311 1555 1555 1.34
LINK C LLP B 311 N TYR B 312 1555 1555 1.36
CISPEP 1 ALA A 246 PRO A 247 0 -5.52
CISPEP 2 ARG A 436 PRO A 437 0 6.85
CISPEP 3 ALA B 246 PRO B 247 0 -7.26
CISPEP 4 ARG B 436 PRO B 437 0 6.26
SITE 1 AC1 8 ALA A 103 TYR A 105 LLP A 311 HOH A 705
SITE 2 AC1 8 HOH A 732 HOH A 775 ASN B 126 HIS B 129
SITE 1 AC2 14 HIS A 201 PHE A 249 LLP A 311 VAL A 496
SITE 2 AC2 14 PHE A 500 PRO B 127 LEU B 128 PRO B 130
SITE 3 AC2 14 TRP B 340 GLY B 342 ILE B 344 TYR B 345
SITE 4 AC2 14 ALA B 346 HOH B 714
SITE 1 AC3 14 LEU A 128 PRO A 130 TRP A 340 GLY A 342
SITE 2 AC3 14 ILE A 344 TYR A 345 ALA A 346 HOH A 712
SITE 3 AC3 14 HOH A 747 HIS B 201 PHE B 249 LLP B 311
SITE 4 AC3 14 SER B 497 PHE B 500
SITE 1 AC4 12 ASN A 126 LEU A 128 HIS A 129 HOH A 712
SITE 2 AC4 12 HOH A 745 ALA B 103 TYR B 105 LLP B 311
SITE 3 AC4 12 HOH B 703 HOH B 738 HOH B 741 HOH B 800
CRYST1 83.940 85.126 129.507 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.011913 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011747 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007722 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
